Starting phenix.real_space_refine on Fri Mar 22 20:16:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tki_41352/03_2024/8tki_41352_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tki_41352/03_2024/8tki_41352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tki_41352/03_2024/8tki_41352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tki_41352/03_2024/8tki_41352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tki_41352/03_2024/8tki_41352_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tki_41352/03_2024/8tki_41352_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 460 5.16 5 C 46468 2.51 5 N 12484 2.21 5 O 13532 1.98 5 H 72844 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1277": "OE1" <-> "OE2" Residue "A PHE 2222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 2496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B ASP 593": "OD1" <-> "OD2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 835": "OE1" <-> "OE2" Residue "B GLU 838": "OE1" <-> "OE2" Residue "B GLU 854": "OE1" <-> "OE2" Residue "B PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 961": "OD1" <-> "OD2" Residue "B GLU 1033": "OE1" <-> "OE2" Residue "B PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1125": "OE1" <-> "OE2" Residue "B TYR 1272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1301": "OD1" <-> "OD2" Residue "B GLU 1593": "OE1" <-> "OE2" Residue "B GLU 1625": "OE1" <-> "OE2" Residue "B GLU 1656": "OE1" <-> "OE2" Residue "B PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1783": "OE1" <-> "OE2" Residue "B PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1963": "OE1" <-> "OE2" Residue "B GLU 2011": "OE1" <-> "OE2" Residue "B GLU 2014": "OE1" <-> "OE2" Residue "B ASP 2027": "OD1" <-> "OD2" Residue "B GLU 2037": "OE1" <-> "OE2" Residue "B GLU 2043": "OE1" <-> "OE2" Residue "B GLU 2118": "OE1" <-> "OE2" Residue "B GLU 2150": "OE1" <-> "OE2" Residue "B GLU 2160": "OE1" <-> "OE2" Residue "B GLU 2163": "OE1" <-> "OE2" Residue "B GLU 2183": "OE1" <-> "OE2" Residue "B PHE 2222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2353": "OE1" <-> "OE2" Residue "B GLU 2398": "OE1" <-> "OE2" Residue "B TYR 2496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2556": "OE1" <-> "OE2" Residue "B GLU 2557": "OE1" <-> "OE2" Residue "B GLU 2562": "OE1" <-> "OE2" Residue "B PHE 2571": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2582": "OD1" <-> "OD2" Residue "C ASP 203": "OD1" <-> "OD2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 511": "OE1" <-> "OE2" Residue "C GLU 539": "OE1" <-> "OE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C GLU 838": "OE1" <-> "OE2" Residue "C GLU 854": "OE1" <-> "OE2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1625": "OE1" <-> "OE2" Residue "C GLU 1656": "OE1" <-> "OE2" Residue "C ASP 1762": "OD1" <-> "OD2" Residue "C GLU 1767": "OE1" <-> "OE2" Residue "C GLU 1783": "OE1" <-> "OE2" Residue "C GLU 1931": "OE1" <-> "OE2" Residue "C GLU 1963": "OE1" <-> "OE2" Residue "C GLU 2011": "OE1" <-> "OE2" Residue "C GLU 2014": "OE1" <-> "OE2" Residue "C GLU 2037": "OE1" <-> "OE2" Residue "C GLU 2048": "OE1" <-> "OE2" Residue "C TYR 2116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2149": "OE1" <-> "OE2" Residue "C GLU 2163": "OE1" <-> "OE2" Residue "C GLU 2353": "OE1" <-> "OE2" Residue "C GLU 2398": "OE1" <-> "OE2" Residue "C TYR 2496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2526": "OE1" <-> "OE2" Residue "C PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 424": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 495": "OD1" <-> "OD2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D ASP 593": "OD1" <-> "OD2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D GLU 616": "OE1" <-> "OE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 854": "OE1" <-> "OE2" Residue "D PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 961": "OD1" <-> "OD2" Residue "D GLU 973": "OE1" <-> "OE2" Residue "D GLU 1050": "OE1" <-> "OE2" Residue "D GLU 1125": "OE1" <-> "OE2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D GLU 1593": "OE1" <-> "OE2" Residue "D GLU 1625": "OE1" <-> "OE2" Residue "D PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1963": "OE1" <-> "OE2" Residue "D TYR 1984": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2011": "OE1" <-> "OE2" Residue "D GLU 2014": "OE1" <-> "OE2" Residue "D ASP 2027": "OD1" <-> "OD2" Residue "D GLU 2037": "OE1" <-> "OE2" Residue "D GLU 2118": "OE1" <-> "OE2" Residue "D PHE 2146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2149": "OE1" <-> "OE2" Residue "D GLU 2150": "OE1" <-> "OE2" Residue "D GLU 2160": "OE1" <-> "OE2" Residue "D GLU 2163": "OE1" <-> "OE2" Residue "D ASP 2173": "OD1" <-> "OD2" Residue "D GLU 2183": "OE1" <-> "OE2" Residue "D TYR 2350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2398": "OE1" <-> "OE2" Residue "D TYR 2496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2526": "OE1" <-> "OE2" Residue "D GLU 2532": "OE1" <-> "OE2" Residue "D GLU 2556": "OE1" <-> "OE2" Residue "D PHE 2571": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 2600": "OD1" <-> "OD2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145816 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34872 SG CYS A2538 153.356 137.972 108.356 1.00 40.37 S ATOM 34921 SG CYS A2541 151.302 138.813 106.157 1.00 36.48 S ATOM 71270 SG CYS B2538 129.781 153.372 108.349 1.00 44.40 S ATOM 71319 SG CYS B2541 128.936 151.317 106.152 1.00 42.05 S ATOM A05X0 SG CYS C2538 114.274 129.677 108.327 1.00 43.29 S ATOM A05YD SG CYS C2541 116.327 128.834 106.129 1.00 38.38 S ATOM A0Y02 SG CYS D2538 137.833 114.251 108.352 1.00 35.25 S ATOM A0Y1F SG CYS D2541 138.680 116.306 106.156 1.00 31.83 S Time building chain proxies: 44.31, per 1000 atoms: 0.30 Number of scatterers: 145816 At special positions: 0 Unit cell: (268.45, 269.276, 192.458, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 460 16.00 P 24 15.00 O 13532 8.00 N 12484 7.00 C 46468 6.00 H 72844 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 92.98 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2541 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2538 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B3001 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2541 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2538 " pdb=" ZN C3001 " pdb="ZN ZN C3001 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C3001 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2541 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2538 " pdb=" ZN D3001 " pdb="ZN ZN D3001 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D3001 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2541 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2538 " Number of angles added : 5 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17392 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 416 helices and 40 sheets defined 70.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 32.08 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.219A pdb=" N GLY A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 44' Processing helix chain 'A' and resid 51 through 56 removed outlier: 4.366A pdb=" N CYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 86 through 112 Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.926A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.591A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 277' Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.505A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.709A pdb=" N ASN A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 537 through 542 removed outlier: 4.718A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 565 Proline residue: A 548 - end of helix removed outlier: 3.897A pdb=" N GLU A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 4.382A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 590 through 600 removed outlier: 3.562A pdb=" N THR A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.579A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.912A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.910A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 661 through 666' Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 719 through 741 Processing helix chain 'A' and resid 744 through 755 removed outlier: 3.770A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 767 removed outlier: 5.816A pdb=" N GLU A 767 " --> pdb=" O CYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 811 through 820 removed outlier: 4.392A pdb=" N LEU A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 829 removed outlier: 5.458A pdb=" N LYS A 829 " --> pdb=" O ASP A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 5.311A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 874 Processing helix chain 'A' and resid 877 through 893 removed outlier: 4.101A pdb=" N THR A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 1002 Processing helix chain 'A' and resid 1024 through 1037 removed outlier: 3.728A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLY A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1047 removed outlier: 4.306A pdb=" N SER A1043 " --> pdb=" O GLY A1039 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N MET A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A1045 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1039 through 1047' Processing helix chain 'A' and resid 1052 through 1066 removed outlier: 3.564A pdb=" N HIS A1065 " --> pdb=" O HIS A1061 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.673A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1096 removed outlier: 5.611A pdb=" N GLN A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1124 Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 4.087A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A1172 " --> pdb=" O ASN A1168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 removed outlier: 4.783A pdb=" N ARG A1190 " --> pdb=" O GLY A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1212 removed outlier: 3.803A pdb=" N LEU A1210 " --> pdb=" O MET A1206 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1237 removed outlier: 6.339A pdb=" N MET A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU A1223 " --> pdb=" O ALA A1219 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A1230 " --> pdb=" O ARG A1226 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A1232 " --> pdb=" O THR A1228 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A1237 " --> pdb=" O GLN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 3.516A pdb=" N LYS A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 removed outlier: 4.229A pdb=" N ALA A1261 " --> pdb=" O GLY A1257 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A1263 " --> pdb=" O LEU A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.821A pdb=" N GLU A1277 " --> pdb=" O GLN A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1292 removed outlier: 3.804A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 3.927A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 removed outlier: 3.692A pdb=" N ASN A1327 " --> pdb=" O THR A1323 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A1328 " --> pdb=" O GLU A1324 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 removed outlier: 4.011A pdb=" N ALA A1351 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A1352 " --> pdb=" O MET A1348 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A1353 " --> pdb=" O MET A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 3.577A pdb=" N ALA A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1392 removed outlier: 4.590A pdb=" N GLU A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A1389 " --> pdb=" O ILE A1385 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A1390 " --> pdb=" O LYS A1386 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A1391 " --> pdb=" O CYS A1387 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1393 through 1402 removed outlier: 3.570A pdb=" N HIS A1402 " --> pdb=" O SER A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1428 through 1433 removed outlier: 4.036A pdb=" N TYR A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1458 removed outlier: 5.004A pdb=" N THR A1439 " --> pdb=" O ASN A1435 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A1458 " --> pdb=" O LYS A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.614A pdb=" N VAL A1471 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1488 removed outlier: 4.507A pdb=" N ASN A1487 " --> pdb=" O PRO A1483 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1483 through 1488' Processing helix chain 'A' and resid 1490 through 1512 removed outlier: 4.017A pdb=" N HIS A1494 " --> pdb=" O SER A1490 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN A1495 " --> pdb=" O LEU A1491 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR A1496 " --> pdb=" O GLN A1492 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE A1497 " --> pdb=" O THR A1493 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A1498 " --> pdb=" O HIS A1494 " (cutoff:3.500A) Proline residue: A1512 - end of helix Processing helix chain 'A' and resid 1515 through 1537 removed outlier: 4.051A pdb=" N GLY A1520 " --> pdb=" O GLN A1516 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A1522 " --> pdb=" O HIS A1518 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A1535 " --> pdb=" O MET A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 removed outlier: 3.950A pdb=" N MET A1551 " --> pdb=" O HIS A1547 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A1553 " --> pdb=" O SER A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1624 removed outlier: 3.537A pdb=" N LYS A1607 " --> pdb=" O GLU A1603 " (cutoff:3.500A) Proline residue: A1608 - end of helix Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 Processing helix chain 'A' and resid 1642 through 1655 Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 4.946A pdb=" N LYS A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1695 Processing helix chain 'A' and resid 1717 through 1732 Processing helix chain 'A' and resid 1733 through 1744 Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1765 through 1779 Processing helix chain 'A' and resid 1781 through 1804 Processing helix chain 'A' and resid 1864 through 1882 removed outlier: 3.701A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1894 Processing helix chain 'A' and resid 1902 through 1916 removed outlier: 3.761A pdb=" N GLU A1906 " --> pdb=" O ASN A1902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1923 removed outlier: 4.138A pdb=" N GLY A1923 " --> pdb=" O THR A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 3.674A pdb=" N TYR A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1949 Processing helix chain 'A' and resid 1952 through 1962 Processing helix chain 'A' and resid 1965 through 1976 removed outlier: 3.671A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1985 removed outlier: 3.661A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 Processing helix chain 'A' and resid 2010 through 2021 removed outlier: 3.837A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2040 removed outlier: 3.749A pdb=" N GLU A2036 " --> pdb=" O ALA A2032 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU A2037 " --> pdb=" O TYR A2033 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A2038 " --> pdb=" O LEU A2034 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A2039 " --> pdb=" O GLN A2035 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A2040 " --> pdb=" O GLU A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2064 removed outlier: 4.097A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2073 Proline residue: A2073 - end of helix Processing helix chain 'A' and resid 2112 through 2121 Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 3.942A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A2147 " --> pdb=" O ILE A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2141 through 2147' Processing helix chain 'A' and resid 2148 through 2159 Processing helix chain 'A' and resid 2172 through 2190 removed outlier: 4.382A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2191 through 2222 removed outlier: 3.500A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR A2202 " --> pdb=" O SER A2198 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) Processing helix chain 'A' and resid 2261 through 2276 Processing helix chain 'A' and resid 2277 through 2310 removed outlier: 6.158A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A2310 " --> pdb=" O THR A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2317 Processing helix chain 'A' and resid 2318 through 2336 Processing helix chain 'A' and resid 2337 through 2352 removed outlier: 4.492A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2364 removed outlier: 3.697A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2390 Processing helix chain 'A' and resid 2457 through 2472 removed outlier: 4.154A pdb=" N LEU A2470 " --> pdb=" O MET A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.474A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2536 removed outlier: 4.138A pdb=" N ILE A2512 " --> pdb=" O VAL A2508 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2549 removed outlier: 4.157A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A2549 " --> pdb=" O ARG A2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2544 through 2549' Processing helix chain 'A' and resid 2554 through 2561 Processing helix chain 'A' and resid 2564 through 2578 Processing helix chain 'A' and resid 2584 through 2597 Processing helix chain 'A' and resid 2610 through 2648 removed outlier: 5.010A pdb=" N GLU A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.219A pdb=" N GLY B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 44' Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.365A pdb=" N CYS B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 86 through 112 Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.926A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.592A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 277' Processing helix chain 'B' and resid 435 through 462 removed outlier: 3.506A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.709A pdb=" N ASN B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 527 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.718A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 565 Proline residue: B 548 - end of helix removed outlier: 3.897A pdb=" N GLU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 removed outlier: 4.382A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 590 through 600 removed outlier: 3.562A pdb=" N THR B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 611 through 626 removed outlier: 3.580A pdb=" N VAL B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 640 removed outlier: 3.912A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.909A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 661 through 666' Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 719 through 741 Processing helix chain 'B' and resid 744 through 755 removed outlier: 3.771A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 767 removed outlier: 5.816A pdb=" N GLU B 767 " --> pdb=" O CYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 784 Processing helix chain 'B' and resid 811 through 820 removed outlier: 4.392A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 829 removed outlier: 5.458A pdb=" N LYS B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 removed outlier: 5.311A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 874 Processing helix chain 'B' and resid 877 through 893 removed outlier: 4.100A pdb=" N THR B 887 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 1002 Processing helix chain 'B' and resid 1024 through 1037 removed outlier: 3.728A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY B1037 " --> pdb=" O GLU B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1047 removed outlier: 4.306A pdb=" N SER B1043 " --> pdb=" O GLY B1039 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N MET B1044 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B1045 " --> pdb=" O THR B1041 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B1046 " --> pdb=" O SER B1042 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL B1047 " --> pdb=" O SER B1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1047' Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 3.564A pdb=" N HIS B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP B1066 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.672A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1096 removed outlier: 5.611A pdb=" N GLN B1096 " --> pdb=" O PHE B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1124 Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.087A pdb=" N GLN B1170 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B1171 " --> pdb=" O GLU B1167 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B1172 " --> pdb=" O ASN B1168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1201 removed outlier: 4.784A pdb=" N ARG B1190 " --> pdb=" O GLY B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1212 removed outlier: 3.803A pdb=" N LEU B1210 " --> pdb=" O MET B1206 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B1211 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B1212 " --> pdb=" O ASP B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1218 through 1237 removed outlier: 6.339A pdb=" N MET B1222 " --> pdb=" O ASP B1218 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B1223 " --> pdb=" O ALA B1219 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE B1224 " --> pdb=" O LYS B1220 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN B1230 " --> pdb=" O ARG B1226 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B1232 " --> pdb=" O THR B1228 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B1237 " --> pdb=" O GLN B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 3.516A pdb=" N LYS B1248 " --> pdb=" O ALA B1244 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 removed outlier: 4.229A pdb=" N ALA B1261 " --> pdb=" O GLY B1257 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B1262 " --> pdb=" O LEU B1258 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B1263 " --> pdb=" O LEU B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1271 through 1278 removed outlier: 3.821A pdb=" N GLU B1277 " --> pdb=" O GLN B1273 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1292 removed outlier: 3.803A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1309 removed outlier: 3.928A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B1307 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 removed outlier: 3.691A pdb=" N ASN B1327 " --> pdb=" O THR B1323 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B1328 " --> pdb=" O GLU B1324 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY B1329 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1353 removed outlier: 4.012A pdb=" N ALA B1351 " --> pdb=" O ASP B1347 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B1352 " --> pdb=" O MET B1348 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B1353 " --> pdb=" O MET B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 3.577A pdb=" N ALA B1376 " --> pdb=" O LEU B1372 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1392 removed outlier: 4.590A pdb=" N GLU B1384 " --> pdb=" O ASN B1380 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B1389 " --> pdb=" O ILE B1385 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B1390 " --> pdb=" O LYS B1386 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B1391 " --> pdb=" O CYS B1387 " (cutoff:3.500A) Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1402 removed outlier: 3.570A pdb=" N HIS B1402 " --> pdb=" O SER B1398 " (cutoff:3.500A) Processing helix chain 'B' and resid 1406 through 1420 Processing helix chain 'B' and resid 1428 through 1433 removed outlier: 4.036A pdb=" N TYR B1432 " --> pdb=" O MET B1428 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1458 removed outlier: 5.004A pdb=" N THR B1439 " --> pdb=" O ASN B1435 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B1458 " --> pdb=" O LYS B1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.613A pdb=" N VAL B1471 " --> pdb=" O TYR B1467 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B1474 " --> pdb=" O SER B1470 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B1482 " --> pdb=" O ALA B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1483 through 1488 removed outlier: 4.507A pdb=" N ASN B1487 " --> pdb=" O PRO B1483 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1483 through 1488' Processing helix chain 'B' and resid 1490 through 1512 removed outlier: 4.017A pdb=" N HIS B1494 " --> pdb=" O SER B1490 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN B1495 " --> pdb=" O LEU B1491 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1496 " --> pdb=" O GLN B1492 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE B1497 " --> pdb=" O THR B1493 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL B1498 " --> pdb=" O HIS B1494 " (cutoff:3.500A) Proline residue: B1512 - end of helix Processing helix chain 'B' and resid 1515 through 1537 removed outlier: 4.051A pdb=" N GLY B1520 " --> pdb=" O GLN B1516 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER B1521 " --> pdb=" O GLN B1517 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B1522 " --> pdb=" O HIS B1518 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B1535 " --> pdb=" O MET B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1553 removed outlier: 3.951A pdb=" N MET B1551 " --> pdb=" O HIS B1547 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B1553 " --> pdb=" O SER B1549 " (cutoff:3.500A) Processing helix chain 'B' and resid 1587 through 1624 removed outlier: 3.537A pdb=" N LYS B1607 " --> pdb=" O GLU B1603 " (cutoff:3.500A) Proline residue: B1608 - end of helix Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 Processing helix chain 'B' and resid 1642 through 1655 Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 4.946A pdb=" N LYS B1675 " --> pdb=" O GLN B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1695 Processing helix chain 'B' and resid 1717 through 1732 Processing helix chain 'B' and resid 1733 through 1744 Processing helix chain 'B' and resid 1746 through 1762 Processing helix chain 'B' and resid 1765 through 1779 Processing helix chain 'B' and resid 1781 through 1804 Processing helix chain 'B' and resid 1864 through 1882 removed outlier: 3.701A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1885 through 1894 Processing helix chain 'B' and resid 1902 through 1916 removed outlier: 3.761A pdb=" N GLU B1906 " --> pdb=" O ASN B1902 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 4.138A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 3.674A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1949 Processing helix chain 'B' and resid 1952 through 1962 Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 3.671A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1985 removed outlier: 3.662A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 Processing helix chain 'B' and resid 2010 through 2021 removed outlier: 3.837A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2040 removed outlier: 3.749A pdb=" N GLU B2036 " --> pdb=" O ALA B2032 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU B2037 " --> pdb=" O TYR B2033 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B2038 " --> pdb=" O LEU B2034 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B2039 " --> pdb=" O GLN B2035 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU B2040 " --> pdb=" O GLU B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2064 removed outlier: 4.097A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) Processing helix chain 'B' and resid 2065 through 2073 Proline residue: B2073 - end of helix Processing helix chain 'B' and resid 2112 through 2121 Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 3.942A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU B2147 " --> pdb=" O ILE B2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2141 through 2147' Processing helix chain 'B' and resid 2148 through 2159 Processing helix chain 'B' and resid 2172 through 2190 removed outlier: 4.382A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 2191 through 2222 removed outlier: 3.500A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) Processing helix chain 'B' and resid 2261 through 2276 Processing helix chain 'B' and resid 2277 through 2310 removed outlier: 6.158A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B2310 " --> pdb=" O THR B2306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2317 Processing helix chain 'B' and resid 2318 through 2336 Processing helix chain 'B' and resid 2337 through 2352 removed outlier: 4.492A pdb=" N TYR B2341 " --> pdb=" O HIS B2337 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER B2342 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) Processing helix chain 'B' and resid 2353 through 2364 removed outlier: 3.697A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2390 Processing helix chain 'B' and resid 2457 through 2472 removed outlier: 4.154A pdb=" N LEU B2470 " --> pdb=" O MET B2466 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.475A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2536 removed outlier: 4.138A pdb=" N ILE B2512 " --> pdb=" O VAL B2508 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.157A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B2549 " --> pdb=" O ARG B2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2544 through 2549' Processing helix chain 'B' and resid 2554 through 2561 Processing helix chain 'B' and resid 2564 through 2578 Processing helix chain 'B' and resid 2584 through 2597 Processing helix chain 'B' and resid 2610 through 2648 removed outlier: 5.010A pdb=" N GLU B2614 " --> pdb=" O LEU B2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 4.220A pdb=" N GLY C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 44' Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.365A pdb=" N CYS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 86 through 112 Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.926A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.592A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 277' Processing helix chain 'C' and resid 435 through 462 removed outlier: 3.505A pdb=" N ILE C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 513 removed outlier: 3.709A pdb=" N ASN C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 527 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 537 through 542 removed outlier: 4.717A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 565 Proline residue: C 548 - end of helix removed outlier: 3.898A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 4.382A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 590 through 600 removed outlier: 3.563A pdb=" N THR C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 610 Processing helix chain 'C' and resid 611 through 626 removed outlier: 3.579A pdb=" N VAL C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.912A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 Processing helix chain 'C' and resid 661 through 666 removed outlier: 3.910A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 661 through 666' Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 719 through 741 Processing helix chain 'C' and resid 744 through 755 removed outlier: 3.771A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 767 removed outlier: 5.816A pdb=" N GLU C 767 " --> pdb=" O CYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 811 through 820 removed outlier: 4.392A pdb=" N LEU C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 829 removed outlier: 5.458A pdb=" N LYS C 829 " --> pdb=" O ASP C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 848 removed outlier: 5.312A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 874 Processing helix chain 'C' and resid 877 through 893 removed outlier: 4.100A pdb=" N THR C 887 " --> pdb=" O ARG C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 1002 Processing helix chain 'C' and resid 1024 through 1037 removed outlier: 3.727A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1047 removed outlier: 4.306A pdb=" N SER C1043 " --> pdb=" O GLY C1039 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N MET C1044 " --> pdb=" O LYS C1040 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C1045 " --> pdb=" O THR C1041 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL C1047 " --> pdb=" O SER C1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1039 through 1047' Processing helix chain 'C' and resid 1052 through 1066 removed outlier: 3.563A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.672A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1096 removed outlier: 5.610A pdb=" N GLN C1096 " --> pdb=" O PHE C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1124 Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 4.087A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1201 removed outlier: 4.783A pdb=" N ARG C1190 " --> pdb=" O GLY C1186 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1212 removed outlier: 3.803A pdb=" N LEU C1210 " --> pdb=" O MET C1206 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C1211 " --> pdb=" O LEU C1207 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C1212 " --> pdb=" O ASP C1208 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1237 removed outlier: 6.339A pdb=" N MET C1222 " --> pdb=" O ASP C1218 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU C1223 " --> pdb=" O ALA C1219 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE C1224 " --> pdb=" O LYS C1220 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C1230 " --> pdb=" O ARG C1226 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C1232 " --> pdb=" O THR C1228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C1237 " --> pdb=" O GLN C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 3.516A pdb=" N LYS C1248 " --> pdb=" O ALA C1244 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 removed outlier: 4.230A pdb=" N ALA C1261 " --> pdb=" O GLY C1257 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C1262 " --> pdb=" O LEU C1258 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C1263 " --> pdb=" O LEU C1259 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1278 removed outlier: 3.821A pdb=" N GLU C1277 " --> pdb=" O GLN C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1292 removed outlier: 3.804A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 3.927A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C1307 " --> pdb=" O LEU C1303 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 removed outlier: 3.691A pdb=" N ASN C1327 " --> pdb=" O THR C1323 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C1328 " --> pdb=" O GLU C1324 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1353 removed outlier: 4.011A pdb=" N ALA C1351 " --> pdb=" O ASP C1347 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C1352 " --> pdb=" O MET C1348 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C1353 " --> pdb=" O MET C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1360 through 1378 removed outlier: 3.577A pdb=" N ALA C1376 " --> pdb=" O LEU C1372 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY C1378 " --> pdb=" O ALA C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1380 through 1392 removed outlier: 4.590A pdb=" N GLU C1384 " --> pdb=" O ASN C1380 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C1385 " --> pdb=" O VAL C1381 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C1389 " --> pdb=" O ILE C1385 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU C1390 " --> pdb=" O LYS C1386 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C1391 " --> pdb=" O CYS C1387 " (cutoff:3.500A) Proline residue: C1392 - end of helix Processing helix chain 'C' and resid 1393 through 1402 removed outlier: 3.570A pdb=" N HIS C1402 " --> pdb=" O SER C1398 " (cutoff:3.500A) Processing helix chain 'C' and resid 1406 through 1420 Processing helix chain 'C' and resid 1428 through 1433 removed outlier: 4.036A pdb=" N TYR C1432 " --> pdb=" O MET C1428 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1458 removed outlier: 5.005A pdb=" N THR C1439 " --> pdb=" O ASN C1435 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C1458 " --> pdb=" O LYS C1454 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.614A pdb=" N VAL C1471 " --> pdb=" O TYR C1467 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C1474 " --> pdb=" O SER C1470 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C1482 " --> pdb=" O ALA C1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 1483 through 1488 removed outlier: 4.508A pdb=" N ASN C1487 " --> pdb=" O PRO C1483 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER C1488 " --> pdb=" O PHE C1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1483 through 1488' Processing helix chain 'C' and resid 1490 through 1512 removed outlier: 4.017A pdb=" N HIS C1494 " --> pdb=" O SER C1490 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN C1495 " --> pdb=" O LEU C1491 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1496 " --> pdb=" O GLN C1492 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE C1497 " --> pdb=" O THR C1493 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL C1498 " --> pdb=" O HIS C1494 " (cutoff:3.500A) Proline residue: C1512 - end of helix Processing helix chain 'C' and resid 1515 through 1537 removed outlier: 4.051A pdb=" N GLY C1520 " --> pdb=" O GLN C1516 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER C1521 " --> pdb=" O GLN C1517 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL C1522 " --> pdb=" O HIS C1518 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C1535 " --> pdb=" O MET C1531 " (cutoff:3.500A) Processing helix chain 'C' and resid 1541 through 1553 removed outlier: 3.950A pdb=" N MET C1551 " --> pdb=" O HIS C1547 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER C1553 " --> pdb=" O SER C1549 " (cutoff:3.500A) Processing helix chain 'C' and resid 1587 through 1624 removed outlier: 3.538A pdb=" N LYS C1607 " --> pdb=" O GLU C1603 " (cutoff:3.500A) Proline residue: C1608 - end of helix Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 Processing helix chain 'C' and resid 1642 through 1655 Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 4.946A pdb=" N LYS C1675 " --> pdb=" O GLN C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1695 Processing helix chain 'C' and resid 1717 through 1732 Processing helix chain 'C' and resid 1733 through 1744 Processing helix chain 'C' and resid 1746 through 1762 Processing helix chain 'C' and resid 1765 through 1779 Processing helix chain 'C' and resid 1781 through 1804 Processing helix chain 'C' and resid 1864 through 1882 removed outlier: 3.700A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1885 through 1894 Processing helix chain 'C' and resid 1902 through 1916 removed outlier: 3.761A pdb=" N GLU C1906 " --> pdb=" O ASN C1902 " (cutoff:3.500A) Processing helix chain 'C' and resid 1917 through 1923 removed outlier: 4.139A pdb=" N GLY C1923 " --> pdb=" O THR C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 3.674A pdb=" N TYR C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1949 Processing helix chain 'C' and resid 1952 through 1962 Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 3.671A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1985 removed outlier: 3.661A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 Processing helix chain 'C' and resid 2010 through 2021 removed outlier: 3.836A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2040 removed outlier: 3.749A pdb=" N GLU C2036 " --> pdb=" O ALA C2032 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU C2037 " --> pdb=" O TYR C2033 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU C2038 " --> pdb=" O LEU C2034 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG C2039 " --> pdb=" O GLN C2035 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU C2040 " --> pdb=" O GLU C2036 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2064 removed outlier: 4.097A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) Processing helix chain 'C' and resid 2065 through 2073 Proline residue: C2073 - end of helix Processing helix chain 'C' and resid 2112 through 2121 Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 3.942A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C2147 " --> pdb=" O ILE C2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2141 through 2147' Processing helix chain 'C' and resid 2148 through 2159 Processing helix chain 'C' and resid 2172 through 2190 removed outlier: 4.382A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) Processing helix chain 'C' and resid 2191 through 2222 removed outlier: 3.573A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) Processing helix chain 'C' and resid 2261 through 2276 Processing helix chain 'C' and resid 2277 through 2310 removed outlier: 6.158A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C2310 " --> pdb=" O THR C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2317 Processing helix chain 'C' and resid 2318 through 2336 Processing helix chain 'C' and resid 2337 through 2352 removed outlier: 4.492A pdb=" N TYR C2341 " --> pdb=" O HIS C2337 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER C2342 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2353 through 2364 removed outlier: 3.698A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2390 Processing helix chain 'C' and resid 2457 through 2472 removed outlier: 4.154A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.475A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2536 removed outlier: 4.138A pdb=" N ILE C2512 " --> pdb=" O VAL C2508 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.158A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2544 through 2549' Processing helix chain 'C' and resid 2554 through 2561 Processing helix chain 'C' and resid 2564 through 2578 Processing helix chain 'C' and resid 2584 through 2597 Processing helix chain 'C' and resid 2610 through 2648 removed outlier: 5.010A pdb=" N GLU C2614 " --> pdb=" O LEU C2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 4.220A pdb=" N GLY D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 39 through 44' Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.366A pdb=" N CYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 86 through 112 Processing helix chain 'D' and resid 226 through 231 removed outlier: 4.926A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.591A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N THR D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 277' Processing helix chain 'D' and resid 435 through 462 removed outlier: 3.504A pdb=" N ILE D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.708A pdb=" N ASN D 513 " --> pdb=" O MET D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 527 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 537 through 542 removed outlier: 4.718A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 565 Proline residue: D 548 - end of helix removed outlier: 3.897A pdb=" N GLU D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 4.382A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 585 Processing helix chain 'D' and resid 590 through 600 removed outlier: 3.562A pdb=" N THR D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 610 Processing helix chain 'D' and resid 611 through 626 removed outlier: 3.580A pdb=" N VAL D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 640 removed outlier: 3.913A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 657 Processing helix chain 'D' and resid 661 through 666 removed outlier: 3.910A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 661 through 666' Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 719 through 741 Processing helix chain 'D' and resid 744 through 755 removed outlier: 3.770A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 767 removed outlier: 5.817A pdb=" N GLU D 767 " --> pdb=" O CYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 784 Processing helix chain 'D' and resid 811 through 820 removed outlier: 4.392A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 829 removed outlier: 5.458A pdb=" N LYS D 829 " --> pdb=" O ASP D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 848 removed outlier: 5.312A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 874 Processing helix chain 'D' and resid 877 through 893 removed outlier: 4.101A pdb=" N THR D 887 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 1002 Processing helix chain 'D' and resid 1024 through 1037 removed outlier: 3.728A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLY D1037 " --> pdb=" O GLU D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1047 removed outlier: 4.307A pdb=" N SER D1043 " --> pdb=" O GLY D1039 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N MET D1044 " --> pdb=" O LYS D1040 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU D1045 " --> pdb=" O THR D1041 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D1046 " --> pdb=" O SER D1042 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL D1047 " --> pdb=" O SER D1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1039 through 1047' Processing helix chain 'D' and resid 1052 through 1066 removed outlier: 3.564A pdb=" N HIS D1065 " --> pdb=" O HIS D1061 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP D1066 " --> pdb=" O LEU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.673A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1096 removed outlier: 5.612A pdb=" N GLN D1096 " --> pdb=" O PHE D1092 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1124 Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 4.087A pdb=" N GLN D1170 " --> pdb=" O SER D1166 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE D1171 " --> pdb=" O GLU D1167 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL D1172 " --> pdb=" O ASN D1168 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1201 removed outlier: 4.784A pdb=" N ARG D1190 " --> pdb=" O GLY D1186 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1212 removed outlier: 3.803A pdb=" N LEU D1210 " --> pdb=" O MET D1206 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D1211 " --> pdb=" O LEU D1207 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D1212 " --> pdb=" O ASP D1208 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1237 removed outlier: 6.339A pdb=" N MET D1222 " --> pdb=" O ASP D1218 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU D1223 " --> pdb=" O ALA D1219 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE D1224 " --> pdb=" O LYS D1220 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN D1230 " --> pdb=" O ARG D1226 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D1232 " --> pdb=" O THR D1228 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D1237 " --> pdb=" O GLN D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 3.516A pdb=" N LYS D1248 " --> pdb=" O ALA D1244 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 removed outlier: 4.229A pdb=" N ALA D1261 " --> pdb=" O GLY D1257 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D1262 " --> pdb=" O LEU D1258 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR D1263 " --> pdb=" O LEU D1259 " (cutoff:3.500A) Processing helix chain 'D' and resid 1271 through 1278 removed outlier: 3.821A pdb=" N GLU D1277 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1292 removed outlier: 3.804A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1309 removed outlier: 3.927A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D1307 " --> pdb=" O LEU D1303 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.691A pdb=" N ASN D1327 " --> pdb=" O THR D1323 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D1328 " --> pdb=" O GLU D1324 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 removed outlier: 4.011A pdb=" N ALA D1351 " --> pdb=" O ASP D1347 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D1352 " --> pdb=" O MET D1348 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG D1353 " --> pdb=" O MET D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1378 removed outlier: 3.577A pdb=" N ALA D1376 " --> pdb=" O LEU D1372 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY D1378 " --> pdb=" O ALA D1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1392 removed outlier: 4.589A pdb=" N GLU D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE D1385 " --> pdb=" O VAL D1381 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D1389 " --> pdb=" O ILE D1385 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D1390 " --> pdb=" O LYS D1386 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D1391 " --> pdb=" O CYS D1387 " (cutoff:3.500A) Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1393 through 1402 removed outlier: 3.570A pdb=" N HIS D1402 " --> pdb=" O SER D1398 " (cutoff:3.500A) Processing helix chain 'D' and resid 1406 through 1420 Processing helix chain 'D' and resid 1428 through 1433 removed outlier: 4.037A pdb=" N TYR D1432 " --> pdb=" O MET D1428 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1458 removed outlier: 5.005A pdb=" N THR D1439 " --> pdb=" O ASN D1435 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D1458 " --> pdb=" O LYS D1454 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.613A pdb=" N VAL D1471 " --> pdb=" O TYR D1467 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D1482 " --> pdb=" O ALA D1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 1483 through 1488 removed outlier: 4.507A pdb=" N ASN D1487 " --> pdb=" O PRO D1483 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER D1488 " --> pdb=" O PHE D1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1483 through 1488' Processing helix chain 'D' and resid 1490 through 1512 removed outlier: 4.018A pdb=" N HIS D1494 " --> pdb=" O SER D1490 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN D1495 " --> pdb=" O LEU D1491 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR D1496 " --> pdb=" O GLN D1492 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE D1497 " --> pdb=" O THR D1493 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL D1498 " --> pdb=" O HIS D1494 " (cutoff:3.500A) Proline residue: D1512 - end of helix Processing helix chain 'D' and resid 1515 through 1537 removed outlier: 4.051A pdb=" N GLY D1520 " --> pdb=" O GLN D1516 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER D1521 " --> pdb=" O GLN D1517 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D1522 " --> pdb=" O HIS D1518 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY D1535 " --> pdb=" O MET D1531 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1553 removed outlier: 3.950A pdb=" N MET D1551 " --> pdb=" O HIS D1547 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER D1553 " --> pdb=" O SER D1549 " (cutoff:3.500A) Processing helix chain 'D' and resid 1587 through 1624 removed outlier: 3.537A pdb=" N LYS D1607 " --> pdb=" O GLU D1603 " (cutoff:3.500A) Proline residue: D1608 - end of helix Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 Processing helix chain 'D' and resid 1642 through 1655 Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 4.945A pdb=" N LYS D1675 " --> pdb=" O GLN D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1695 Processing helix chain 'D' and resid 1717 through 1732 Processing helix chain 'D' and resid 1733 through 1744 Processing helix chain 'D' and resid 1746 through 1762 Processing helix chain 'D' and resid 1765 through 1779 Processing helix chain 'D' and resid 1781 through 1804 Processing helix chain 'D' and resid 1864 through 1882 removed outlier: 3.701A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1894 Processing helix chain 'D' and resid 1902 through 1916 removed outlier: 3.762A pdb=" N GLU D1906 " --> pdb=" O ASN D1902 " (cutoff:3.500A) Processing helix chain 'D' and resid 1917 through 1923 removed outlier: 4.138A pdb=" N GLY D1923 " --> pdb=" O THR D1919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 3.674A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1949 Processing helix chain 'D' and resid 1952 through 1962 Processing helix chain 'D' and resid 1965 through 1976 removed outlier: 3.670A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) Processing helix chain 'D' and resid 1978 through 1985 removed outlier: 3.661A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 Processing helix chain 'D' and resid 2010 through 2021 removed outlier: 3.837A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2040 removed outlier: 3.749A pdb=" N GLU D2036 " --> pdb=" O ALA D2032 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU D2037 " --> pdb=" O TYR D2033 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU D2038 " --> pdb=" O LEU D2034 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG D2039 " --> pdb=" O GLN D2035 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU D2040 " --> pdb=" O GLU D2036 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2064 removed outlier: 4.098A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) Processing helix chain 'D' and resid 2065 through 2073 Proline residue: D2073 - end of helix Processing helix chain 'D' and resid 2112 through 2121 Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 3.943A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D2147 " --> pdb=" O ILE D2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2141 through 2147' Processing helix chain 'D' and resid 2148 through 2159 Processing helix chain 'D' and resid 2172 through 2190 removed outlier: 4.382A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) Processing helix chain 'D' and resid 2191 through 2222 removed outlier: 3.501A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) Processing helix chain 'D' and resid 2261 through 2276 Processing helix chain 'D' and resid 2277 through 2310 removed outlier: 6.158A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY D2310 " --> pdb=" O THR D2306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2317 Processing helix chain 'D' and resid 2318 through 2336 Processing helix chain 'D' and resid 2337 through 2352 removed outlier: 4.492A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) Processing helix chain 'D' and resid 2353 through 2364 removed outlier: 3.697A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2390 Processing helix chain 'D' and resid 2457 through 2472 removed outlier: 4.154A pdb=" N LEU D2470 " --> pdb=" O MET D2466 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2481 removed outlier: 4.475A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2536 removed outlier: 4.138A pdb=" N ILE D2512 " --> pdb=" O VAL D2508 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2549 removed outlier: 4.157A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D2549 " --> pdb=" O ARG D2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2544 through 2549' Processing helix chain 'D' and resid 2554 through 2561 Processing helix chain 'D' and resid 2564 through 2578 Processing helix chain 'D' and resid 2584 through 2597 Processing helix chain 'D' and resid 2610 through 2648 removed outlier: 5.010A pdb=" N GLU D2614 " --> pdb=" O LEU D2610 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 14 through 18 Processing sheet with id= 2, first strand: chain 'A' and resid 57 through 62 removed outlier: 13.600A pdb=" N ILE A 122 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL A 135 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 131 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 161 through 166 removed outlier: 8.395A pdb=" N TRP A 161 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 262 through 265 removed outlier: 5.399A pdb=" N LEU A 243 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N CYS A 254 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 13.659A pdb=" N VAL A 241 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 239 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU A 282 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 309 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 15.041A pdb=" N TYR A 304 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N ALA A 317 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE A 306 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 313 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 367 through 371 Processing sheet with id= 6, first strand: chain 'A' and resid 396 through 402 removed outlier: 3.843A pdb=" N MET A 416 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 667 through 672 removed outlier: 4.057A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 2122 through 2127 Processing sheet with id= 9, first strand: chain 'A' and resid 2395 through 2399 removed outlier: 7.242A pdb=" N PHE A2395 " --> pdb=" O ALA A2454 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER A2450 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= 11, first strand: chain 'B' and resid 14 through 18 Processing sheet with id= 12, first strand: chain 'B' and resid 57 through 62 removed outlier: 13.601A pdb=" N ILE B 122 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL B 135 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU B 124 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 131 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 161 through 166 removed outlier: 8.395A pdb=" N TRP B 161 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 262 through 265 removed outlier: 5.398A pdb=" N LEU B 243 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N CYS B 254 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 13.659A pdb=" N VAL B 241 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP B 239 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU B 282 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 309 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 15.040A pdb=" N TYR B 304 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N ALA B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE B 306 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN B 313 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 367 through 371 Processing sheet with id= 16, first strand: chain 'B' and resid 396 through 402 removed outlier: 3.843A pdb=" N MET B 416 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 667 through 672 removed outlier: 4.056A pdb=" N GLU B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 2122 through 2127 Processing sheet with id= 19, first strand: chain 'B' and resid 2395 through 2399 removed outlier: 7.242A pdb=" N PHE B2395 " --> pdb=" O ALA B2454 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER B2450 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 241 through 245 Processing sheet with id= 21, first strand: chain 'C' and resid 14 through 18 Processing sheet with id= 22, first strand: chain 'C' and resid 57 through 62 removed outlier: 13.600A pdb=" N ILE C 122 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL C 135 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU C 124 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 131 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 161 through 166 removed outlier: 8.395A pdb=" N TRP C 161 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 262 through 265 removed outlier: 5.398A pdb=" N LEU C 243 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N CYS C 254 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 13.659A pdb=" N VAL C 241 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 239 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU C 282 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 309 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 15.041A pdb=" N TYR C 304 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N ALA C 317 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE C 306 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN C 313 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 367 through 371 Processing sheet with id= 26, first strand: chain 'C' and resid 396 through 402 removed outlier: 3.844A pdb=" N MET C 416 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 667 through 672 removed outlier: 4.057A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 2122 through 2127 Processing sheet with id= 29, first strand: chain 'C' and resid 2395 through 2399 removed outlier: 7.241A pdb=" N PHE C2395 " --> pdb=" O ALA C2454 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER C2450 " --> pdb=" O VAL C2399 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 241 through 245 Processing sheet with id= 31, first strand: chain 'D' and resid 14 through 18 Processing sheet with id= 32, first strand: chain 'D' and resid 57 through 62 removed outlier: 13.601A pdb=" N ILE D 122 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL D 135 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 131 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 161 through 166 removed outlier: 8.394A pdb=" N TRP D 161 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 262 through 265 removed outlier: 5.399A pdb=" N LEU D 243 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N CYS D 254 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 13.659A pdb=" N VAL D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP D 239 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU D 282 " --> pdb=" O LEU D 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 309 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 15.040A pdb=" N TYR D 304 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N ALA D 317 " --> pdb=" O TYR D 304 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE D 306 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN D 313 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 367 through 371 Processing sheet with id= 36, first strand: chain 'D' and resid 396 through 402 removed outlier: 3.843A pdb=" N MET D 416 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 667 through 672 removed outlier: 4.057A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 2122 through 2127 Processing sheet with id= 39, first strand: chain 'D' and resid 2395 through 2399 removed outlier: 7.242A pdb=" N PHE D2395 " --> pdb=" O ALA D2454 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER D2450 " --> pdb=" O VAL D2399 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 241 through 245 4329 hydrogen bonds defined for protein. 12963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 66.38 Time building geometry restraints manager: 98.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 72676 1.03 - 1.23: 185 1.23 - 1.42: 30555 1.42 - 1.62: 42992 1.62 - 1.82: 748 Bond restraints: 147156 Sorted by residual: bond pdb=" N PRO B2586 " pdb=" CD PRO B2586 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.41e+01 bond pdb=" N PRO D2586 " pdb=" CD PRO D2586 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" CB PHE B 836 " pdb=" CG PHE B 836 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.12e+00 bond pdb=" CB PHE D 836 " pdb=" CG PHE D 836 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.12e+00 bond pdb=" CB PHE A 836 " pdb=" CG PHE A 836 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.12e+00 ... (remaining 147151 not shown) Histogram of bond angle deviations from ideal: 99.58 - 107.65: 9468 107.65 - 115.72: 180664 115.72 - 123.79: 64826 123.79 - 131.85: 11110 131.85 - 139.92: 96 Bond angle restraints: 266164 Sorted by residual: angle pdb=" CB MET C 965 " pdb=" CG MET C 965 " pdb=" SD MET C 965 " ideal model delta sigma weight residual 112.70 121.08 -8.38 3.00e+00 1.11e-01 7.80e+00 angle pdb=" CB MET A 965 " pdb=" CG MET A 965 " pdb=" SD MET A 965 " ideal model delta sigma weight residual 112.70 121.05 -8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" CB MET D 965 " pdb=" CG MET D 965 " pdb=" SD MET D 965 " ideal model delta sigma weight residual 112.70 121.05 -8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" CB MET B 965 " pdb=" CG MET B 965 " pdb=" SD MET B 965 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.69e+00 angle pdb=" CA MET A1320 " pdb=" CB MET A1320 " pdb=" CG MET A1320 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.07e+00 ... (remaining 266159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.37: 64208 24.37 - 48.73: 3852 48.73 - 73.10: 706 73.10 - 97.46: 94 97.46 - 121.83: 16 Dihedral angle restraints: 68876 sinusoidal: 37668 harmonic: 31208 Sorted by residual: dihedral pdb=" C1 I3P B3002 " pdb=" C2 I3P B3002 " pdb=" C3 I3P B3002 " pdb=" C4 I3P B3002 " ideal model delta sinusoidal sigma weight residual 56.81 -65.02 121.83 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1 I3P C3002 " pdb=" C2 I3P C3002 " pdb=" C3 I3P C3002 " pdb=" C4 I3P C3002 " ideal model delta sinusoidal sigma weight residual 56.81 -65.01 121.82 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1 I3P C3002 " pdb=" C2 I3P C3002 " pdb=" C3 I3P C3002 " pdb=" O3 I3P C3002 " ideal model delta sinusoidal sigma weight residual 177.78 55.96 121.82 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 68873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 10317 0.058 - 0.117: 1144 0.117 - 0.175: 75 0.175 - 0.234: 4 0.234 - 0.292: 8 Chirality restraints: 11548 Sorted by residual: chirality pdb=" C2' ATP A3003 " pdb=" C1' ATP A3003 " pdb=" C3' ATP A3003 " pdb=" O2' ATP A3003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP C3003 " pdb=" C1' ATP C3003 " pdb=" C3' ATP C3003 " pdb=" O2' ATP C3003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP D3003 " pdb=" C1' ATP D3003 " pdb=" C3' ATP D3003 " pdb=" O2' ATP D3003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 11545 not shown) Planarity restraints: 21516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 806 " 0.060 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO A 807 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 743 " 0.139 9.50e-02 1.11e+02 4.70e-02 3.50e+00 pdb=" NE ARG C 743 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 743 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 743 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 743 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 743 " -0.015 2.00e-02 2.50e+03 pdb="HH12 ARG C 743 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG C 743 " -0.011 2.00e-02 2.50e+03 pdb="HH22 ARG C 743 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 883 " -0.134 9.50e-02 1.11e+02 4.53e-02 3.11e+00 pdb=" NE ARG A 883 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 883 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 883 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 883 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 883 " 0.012 2.00e-02 2.50e+03 pdb="HH12 ARG A 883 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 883 " 0.010 2.00e-02 2.50e+03 pdb="HH22 ARG A 883 " -0.006 2.00e-02 2.50e+03 ... (remaining 21513 not shown) Histogram of nonbonded interaction distances: 0.43 - 1.26: 48 1.26 - 2.10: 3906 2.10 - 2.93: 400754 2.93 - 3.77: 625752 3.77 - 4.60: 1047897 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2078357 Sorted by model distance: nonbonded pdb="HH22 ARG A 138 " pdb=" HE1 HIS B1288 " model vdw 0.427 2.100 nonbonded pdb="HH22 ARG B 138 " pdb=" HE1 HIS C1288 " model vdw 0.575 2.100 nonbonded pdb=" HE1 HIS A1288 " pdb="HH22 ARG D 138 " model vdw 0.576 2.100 nonbonded pdb=" HG CYS D1982 " pdb=" HZ2 LYS D1983 " model vdw 0.624 2.270 nonbonded pdb=" HB2 LEU A2355 " pdb="HD21 LEU D2371 " model vdw 0.746 2.440 ... (remaining 2078352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 1.530 Extract box with map and model: 30.270 Check model and map are aligned: 1.570 Set scattering table: 0.970 Process input model: 405.700 Find NCS groups from input model: 5.530 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 454.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 74312 Z= 0.138 Angle : 0.473 8.376 100488 Z= 0.245 Chirality : 0.036 0.292 11548 Planarity : 0.003 0.093 12756 Dihedral : 16.759 121.825 27860 Min Nonbonded Distance : 0.845 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.07 % Allowed : 18.41 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.09), residues: 8952 helix: 2.76 (0.07), residues: 5588 sheet: 0.45 (0.21), residues: 632 loop : 0.62 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D1438 HIS 0.005 0.001 HIS C 703 PHE 0.020 0.001 PHE D 861 TYR 0.012 0.001 TYR B 352 ARG 0.009 0.000 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 1035 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1029 time to evaluate : 8.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1551 MET cc_start: 0.3612 (tpp) cc_final: 0.2779 (pmm) REVERT: A 1992 LEU cc_start: 0.7946 (tp) cc_final: 0.7617 (tp) REVERT: B 1551 MET cc_start: 0.6132 (mmm) cc_final: 0.4246 (pmm) REVERT: B 1736 LEU cc_start: 0.8590 (tp) cc_final: 0.8297 (tp) REVERT: C 1736 LEU cc_start: 0.8670 (tp) cc_final: 0.8409 (tt) REVERT: C 1911 LEU cc_start: 0.8591 (tp) cc_final: 0.8281 (tp) REVERT: C 1992 LEU cc_start: 0.8022 (tp) cc_final: 0.7712 (tp) REVERT: C 2056 LEU cc_start: 0.8238 (tp) cc_final: 0.8033 (tp) REVERT: C 2289 ASN cc_start: 0.7475 (t0) cc_final: 0.7258 (t0) REVERT: C 2458 LEU cc_start: 0.7560 (tp) cc_final: 0.7325 (tp) REVERT: D 1551 MET cc_start: 0.3755 (mmt) cc_final: 0.2088 (pmm) outliers start: 6 outliers final: 1 residues processed: 1035 average time/residue: 1.7265 time to fit residues: 2972.0412 Evaluate side-chains 661 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 660 time to evaluate : 8.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2571 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 763 optimal weight: 9.9990 chunk 685 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 462 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 chunk 708 optimal weight: 7.9990 chunk 274 optimal weight: 7.9990 chunk 430 optimal weight: 7.9990 chunk 527 optimal weight: 9.9990 chunk 820 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 204 ASN A 222 ASN A 248 GLN A1696 GLN A1884 HIS ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2179 HIS A2528 GLN B 123 GLN B 192 GLN B 222 ASN B 248 GLN B 868 HIS ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1769 GLN B1884 HIS B2069 HIS B2179 HIS B2510 ASN C 192 GLN C 222 ASN C 248 GLN ** C1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1773 HIS ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2179 HIS D 123 GLN D 192 GLN D 222 ASN D 226 GLN D 248 GLN D 301 ASN D 713 GLN ** D1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1769 GLN D1884 HIS D2052 ASN D2179 HIS D2472 ASN D2592 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 74312 Z= 0.420 Angle : 0.633 8.348 100488 Z= 0.347 Chirality : 0.037 0.213 11548 Planarity : 0.004 0.046 12756 Dihedral : 5.720 87.393 9994 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.98 % Allowed : 18.78 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.09), residues: 8952 helix: 2.29 (0.07), residues: 5652 sheet: -0.13 (0.20), residues: 632 loop : 0.27 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 219 HIS 0.009 0.001 HIS D1773 PHE 0.026 0.002 PHE C 244 TYR 0.019 0.002 TYR C2583 ARG 0.007 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 863 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 622 time to evaluate : 8.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6888 (tmm) cc_final: 0.6651 (ttm) REVERT: A 1221 MET cc_start: 0.7128 (ppp) cc_final: 0.6459 (ppp) REVERT: A 1551 MET cc_start: 0.3728 (tpp) cc_final: 0.2917 (pmm) REVERT: A 2309 ARG cc_start: 0.6032 (mmm160) cc_final: 0.5803 (mmm160) REVERT: B 62 MET cc_start: 0.7852 (tmm) cc_final: 0.7605 (tmm) REVERT: B 1551 MET cc_start: 0.6118 (mmm) cc_final: 0.4142 (pmm) REVERT: B 1736 LEU cc_start: 0.8772 (tp) cc_final: 0.8504 (tp) REVERT: B 2040 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: C 1221 MET cc_start: 0.6785 (ppp) cc_final: 0.6018 (ppp) REVERT: D 1551 MET cc_start: 0.3454 (mmt) cc_final: 0.1545 (ptt) outliers start: 241 outliers final: 134 residues processed: 826 average time/residue: 1.7025 time to fit residues: 2409.7764 Evaluate side-chains 681 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 546 time to evaluate : 8.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1048 ASP Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 GLU Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1895 GLN Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain A residue 2608 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1201 ASP Chi-restraints excluded: chain B residue 1239 ASN Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1494 HIS Chi-restraints excluded: chain B residue 1645 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2040 GLU Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 543 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1370 ASP Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1668 THR Chi-restraints excluded: chain C residue 1753 SER Chi-restraints excluded: chain C residue 1771 SER Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1879 LEU Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2161 GLN Chi-restraints excluded: chain C residue 2206 SER Chi-restraints excluded: chain C residue 2218 ILE Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2592 GLN Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1338 ASP Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1542 MET Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1881 CYS Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1930 ASN Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2034 LEU Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2594 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 456 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 683 optimal weight: 0.8980 chunk 559 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 822 optimal weight: 9.9990 chunk 888 optimal weight: 10.0000 chunk 732 optimal weight: 5.9990 chunk 815 optimal weight: 30.0000 chunk 280 optimal weight: 5.9990 chunk 659 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 GLN ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1939 GLN ** A2289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1284 GLN B1939 GLN ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN D 785 HIS ** D 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 74312 Z= 0.174 Angle : 0.490 6.953 100488 Z= 0.257 Chirality : 0.034 0.160 11548 Planarity : 0.003 0.037 12756 Dihedral : 4.855 88.542 9992 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.77 % Allowed : 19.30 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.09), residues: 8952 helix: 2.71 (0.07), residues: 5660 sheet: -0.12 (0.20), residues: 632 loop : 0.39 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2196 HIS 0.006 0.001 HIS A1288 PHE 0.020 0.001 PHE A2513 TYR 0.011 0.001 TYR D1947 ARG 0.006 0.000 ARG B1195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 709 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 566 time to evaluate : 8.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6835 (tmm) cc_final: 0.6567 (ttm) REVERT: A 1056 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8595 (tt) REVERT: A 1221 MET cc_start: 0.7024 (ppp) cc_final: 0.6203 (ppp) REVERT: A 1551 MET cc_start: 0.3680 (tpp) cc_final: 0.2952 (pmm) REVERT: A 2460 MET cc_start: 0.6629 (tpp) cc_final: 0.6352 (tpp) REVERT: B 62 MET cc_start: 0.7644 (tmm) cc_final: 0.6646 (tmm) REVERT: B 1551 MET cc_start: 0.6054 (mmm) cc_final: 0.4099 (pmm) REVERT: B 1736 LEU cc_start: 0.8751 (tp) cc_final: 0.8484 (tp) REVERT: B 1737 VAL cc_start: 0.8255 (m) cc_final: 0.8027 (t) REVERT: C 1221 MET cc_start: 0.6792 (ppp) cc_final: 0.6106 (ppp) REVERT: C 1736 LEU cc_start: 0.8652 (tp) cc_final: 0.8433 (tt) REVERT: D 1221 MET cc_start: 0.5960 (ppp) cc_final: 0.5690 (ppp) REVERT: D 1551 MET cc_start: 0.3425 (mmt) cc_final: 0.1525 (ptt) outliers start: 143 outliers final: 105 residues processed: 685 average time/residue: 1.6588 time to fit residues: 1930.7670 Evaluate side-chains 636 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 530 time to evaluate : 8.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 GLU Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2201 MET Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain A residue 2608 MET Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1201 ASP Chi-restraints excluded: chain B residue 1239 ASN Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1494 HIS Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 2034 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 700 ASN Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2354 THR Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1339 LYS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1589 LYS Chi-restraints excluded: chain D residue 1602 LEU Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 812 optimal weight: 9.9990 chunk 618 optimal weight: 10.0000 chunk 426 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 392 optimal weight: 2.9990 chunk 552 optimal weight: 8.9990 chunk 825 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 431 optimal weight: 10.0000 chunk 782 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 101 GLN A 301 ASN A1065 HIS ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 832 ASN B1065 HIS ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 ASN D 47 ASN D 186 ASN D 832 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1494 HIS ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1696 GLN D1769 GLN D1939 GLN ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 74312 Z= 0.341 Angle : 0.548 6.968 100488 Z= 0.300 Chirality : 0.035 0.189 11548 Planarity : 0.003 0.040 12756 Dihedral : 4.951 89.759 9992 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.60 % Allowed : 18.73 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.09), residues: 8952 helix: 2.41 (0.07), residues: 5668 sheet: -0.50 (0.20), residues: 580 loop : 0.15 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2196 HIS 0.008 0.001 HIS C1288 PHE 0.037 0.002 PHE C1082 TYR 0.021 0.001 TYR A 989 ARG 0.008 0.000 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 733 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 523 time to evaluate : 8.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6933 (tmm) cc_final: 0.6714 (ttm) REVERT: A 1221 MET cc_start: 0.6996 (ppp) cc_final: 0.6192 (ppp) REVERT: A 1551 MET cc_start: 0.3700 (tpp) cc_final: 0.3123 (pmm) REVERT: A 2460 MET cc_start: 0.6823 (tpp) cc_final: 0.6525 (tpp) REVERT: B 62 MET cc_start: 0.7900 (tmm) cc_final: 0.7472 (tmm) REVERT: B 1551 MET cc_start: 0.6224 (mmm) cc_final: 0.4235 (pmm) REVERT: B 1737 VAL cc_start: 0.8494 (m) cc_final: 0.8163 (t) REVERT: B 2318 MET cc_start: 0.7611 (tmm) cc_final: 0.7391 (ppp) REVERT: B 2460 MET cc_start: 0.6771 (tpp) cc_final: 0.6538 (tpp) REVERT: C 1221 MET cc_start: 0.6602 (ppp) cc_final: 0.5963 (ppp) REVERT: C 2593 MET cc_start: 0.7876 (mmp) cc_final: 0.7538 (mmp) REVERT: D 1551 MET cc_start: 0.3255 (mmt) cc_final: 0.1343 (ptt) REVERT: D 1901 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5660 (m-80) outliers start: 210 outliers final: 160 residues processed: 703 average time/residue: 1.7155 time to fit residues: 2075.6179 Evaluate side-chains 662 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 501 time to evaluate : 8.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 GLU Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1664 LYS Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 1895 GLN Chi-restraints excluded: chain A residue 1901 TYR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2201 MET Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain A residue 2595 LYS Chi-restraints excluded: chain A residue 2608 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1201 ASP Chi-restraints excluded: chain B residue 1226 ARG Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1494 HIS Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 1892 LEU Chi-restraints excluded: chain B residue 1901 TYR Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2034 LEU Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2170 ASP Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 700 ASN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1668 THR Chi-restraints excluded: chain C residue 1753 SER Chi-restraints excluded: chain C residue 1771 SER Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1895 GLN Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2045 SER Chi-restraints excluded: chain C residue 2296 PHE Chi-restraints excluded: chain C residue 2354 THR Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 700 ASN Chi-restraints excluded: chain D residue 701 ASN Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1226 ARG Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1338 ASP Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1589 LYS Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 1892 LEU Chi-restraints excluded: chain D residue 1895 GLN Chi-restraints excluded: chain D residue 1901 TYR Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1930 ASN Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2183 GLU Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2565 MET Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 727 optimal weight: 0.9980 chunk 496 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 650 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 745 optimal weight: 10.0000 chunk 604 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 446 optimal weight: 5.9990 chunk 784 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2289 ASN ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1265 GLN ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1939 GLN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1684 ASN ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 74312 Z= 0.133 Angle : 0.465 6.133 100488 Z= 0.241 Chirality : 0.034 0.155 11548 Planarity : 0.003 0.033 12756 Dihedral : 4.715 85.942 9992 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.71 % Allowed : 19.09 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.09), residues: 8952 helix: 2.83 (0.07), residues: 5668 sheet: -0.27 (0.21), residues: 580 loop : 0.41 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C2196 HIS 0.005 0.001 HIS C1288 PHE 0.024 0.001 PHE A1082 TYR 0.009 0.001 TYR C 872 ARG 0.004 0.000 ARG C2471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 663 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 525 time to evaluate : 8.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6845 (tmm) cc_final: 0.6591 (ttm) REVERT: A 1221 MET cc_start: 0.6878 (ppp) cc_final: 0.6317 (ppp) REVERT: A 1551 MET cc_start: 0.3780 (tpp) cc_final: 0.3004 (pmm) REVERT: A 2460 MET cc_start: 0.6777 (tpp) cc_final: 0.6499 (tpp) REVERT: B 1551 MET cc_start: 0.6187 (mmm) cc_final: 0.4225 (pmm) REVERT: B 1736 LEU cc_start: 0.8827 (tp) cc_final: 0.8594 (tp) REVERT: C 497 MET cc_start: 0.6405 (tmm) cc_final: 0.6100 (tmm) REVERT: C 1221 MET cc_start: 0.6417 (ppp) cc_final: 0.5849 (ppp) REVERT: C 2593 MET cc_start: 0.7685 (mmp) cc_final: 0.7463 (mmp) REVERT: D 1551 MET cc_start: 0.3164 (mmt) cc_final: 0.1275 (ptt) REVERT: D 1901 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5741 (m-80) outliers start: 138 outliers final: 110 residues processed: 634 average time/residue: 1.6186 time to fit residues: 1732.8568 Evaluate side-chains 613 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 502 time to evaluate : 8.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1664 LYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1901 TYR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2201 MET Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1239 ASN Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 1901 TYR Chi-restraints excluded: chain B residue 2034 LEU Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2201 MET Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1621 LEU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1226 ARG Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1320 MET Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1348 MET Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1589 LYS Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1602 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 1895 GLN Chi-restraints excluded: chain D residue 1901 TYR Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 293 optimal weight: 10.0000 chunk 786 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 513 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 874 optimal weight: 8.9990 chunk 726 optimal weight: 6.9990 chunk 404 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 459 optimal weight: 7.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1883 ASN ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 74312 Z= 0.295 Angle : 0.515 7.855 100488 Z= 0.279 Chirality : 0.035 0.154 11548 Planarity : 0.003 0.039 12756 Dihedral : 4.740 85.796 9992 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.19 % Allowed : 18.75 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.09), residues: 8952 helix: 2.59 (0.07), residues: 5676 sheet: -0.42 (0.20), residues: 596 loop : 0.15 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C2196 HIS 0.006 0.001 HIS C2063 PHE 0.018 0.001 PHE A 482 TYR 0.014 0.001 TYR A 17 ARG 0.013 0.000 ARG B1226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 668 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 491 time to evaluate : 8.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1221 MET cc_start: 0.6834 (ppp) cc_final: 0.6300 (ppp) REVERT: A 1551 MET cc_start: 0.3795 (tpp) cc_final: 0.3023 (pmm) REVERT: B 1551 MET cc_start: 0.6166 (mmm) cc_final: 0.4249 (pmm) REVERT: B 2318 MET cc_start: 0.7729 (tmm) cc_final: 0.7511 (ppp) REVERT: C 1221 MET cc_start: 0.6373 (ppp) cc_final: 0.5865 (ppp) REVERT: C 2593 MET cc_start: 0.7820 (mmp) cc_final: 0.7549 (mmp) REVERT: D 1551 MET cc_start: 0.3144 (mmt) cc_final: 0.1239 (ptt) outliers start: 177 outliers final: 150 residues processed: 634 average time/residue: 1.7255 time to fit residues: 1875.4121 Evaluate side-chains 628 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 478 time to evaluate : 8.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 GLU Chi-restraints excluded: chain A residue 1664 LYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1901 TYR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2201 MET Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain A residue 2595 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 838 GLU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1201 ASP Chi-restraints excluded: chain B residue 1222 MET Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 1901 TYR Chi-restraints excluded: chain B residue 1907 THR Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2170 ASP Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 700 ASN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1310 GLU Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1753 SER Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 701 ASN Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1226 ARG Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1320 MET Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1589 LYS Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 1895 GLN Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 843 optimal weight: 9.9990 chunk 98 optimal weight: 0.0670 chunk 498 optimal weight: 0.9990 chunk 638 optimal weight: 10.0000 chunk 494 optimal weight: 2.9990 chunk 736 optimal weight: 0.6980 chunk 488 optimal weight: 8.9990 chunk 871 optimal weight: 9.9990 chunk 545 optimal weight: 1.9990 chunk 531 optimal weight: 0.8980 chunk 402 optimal weight: 8.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1883 ASN ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1769 GLN D1883 ASN ** D1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 74312 Z= 0.129 Angle : 0.461 6.366 100488 Z= 0.238 Chirality : 0.034 0.143 11548 Planarity : 0.003 0.033 12756 Dihedral : 4.543 89.121 9992 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.58 % Allowed : 18.89 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.09), residues: 8952 helix: 2.89 (0.07), residues: 5676 sheet: -0.28 (0.21), residues: 604 loop : 0.38 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C2196 HIS 0.005 0.001 HIS D1622 PHE 0.014 0.001 PHE D2296 TYR 0.010 0.001 TYR C 872 ARG 0.005 0.000 ARG B1226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 636 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 508 time to evaluate : 8.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6836 (tmm) cc_final: 0.6597 (ttm) REVERT: A 1221 MET cc_start: 0.6755 (ppp) cc_final: 0.6443 (ppp) REVERT: A 1551 MET cc_start: 0.3768 (tpp) cc_final: 0.3031 (pmm) REVERT: B 1348 MET cc_start: 0.6719 (ptp) cc_final: 0.6312 (ptm) REVERT: B 1542 MET cc_start: 0.6502 (pmm) cc_final: 0.5840 (pmm) REVERT: B 1551 MET cc_start: 0.6111 (mmm) cc_final: 0.4256 (pmm) REVERT: B 2318 MET cc_start: 0.7700 (tmm) cc_final: 0.7499 (ppp) REVERT: C 497 MET cc_start: 0.6329 (tmm) cc_final: 0.6112 (tmm) REVERT: C 1221 MET cc_start: 0.6237 (ppp) cc_final: 0.5811 (ppp) REVERT: C 2593 MET cc_start: 0.7697 (mmp) cc_final: 0.7467 (mmp) REVERT: D 1551 MET cc_start: 0.3076 (mmt) cc_final: 0.1187 (ptt) outliers start: 128 outliers final: 109 residues processed: 612 average time/residue: 1.6293 time to fit residues: 1691.5613 Evaluate side-chains 602 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 493 time to evaluate : 7.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1664 LYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1901 TYR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2201 MET Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1239 ASN Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 1901 TYR Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 LYS Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1226 ARG Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1320 MET Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1602 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 1895 GLN Chi-restraints excluded: chain D residue 1901 TYR Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 539 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 520 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 553 optimal weight: 6.9990 chunk 593 optimal weight: 3.9990 chunk 430 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 684 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2063 HIS ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1494 HIS D1769 GLN D1883 ASN ** D1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 74312 Z= 0.321 Angle : 0.529 6.445 100488 Z= 0.287 Chirality : 0.035 0.162 11548 Planarity : 0.003 0.049 12756 Dihedral : 4.735 88.902 9992 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.90 % Allowed : 18.75 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.09), residues: 8952 helix: 2.58 (0.07), residues: 5668 sheet: -0.63 (0.20), residues: 636 loop : 0.13 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1127 HIS 0.006 0.001 HIS C1884 PHE 0.020 0.001 PHE A 482 TYR 0.017 0.001 TYR A 17 ARG 0.006 0.000 ARG C1226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 629 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 475 time to evaluate : 8.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6920 (tmm) cc_final: 0.6710 (ttp) REVERT: A 1221 MET cc_start: 0.6825 (ppp) cc_final: 0.6462 (ppp) REVERT: A 1551 MET cc_start: 0.3804 (tpp) cc_final: 0.3060 (pmm) REVERT: B 1348 MET cc_start: 0.6776 (ptp) cc_final: 0.6263 (ptm) REVERT: B 1542 MET cc_start: 0.6592 (pmm) cc_final: 0.5955 (pmm) REVERT: B 1551 MET cc_start: 0.6106 (mmm) cc_final: 0.4139 (pmm) REVERT: B 2460 MET cc_start: 0.6816 (tpp) cc_final: 0.6539 (tpp) REVERT: C 497 MET cc_start: 0.6434 (tmm) cc_final: 0.6158 (tmm) REVERT: C 1221 MET cc_start: 0.6214 (ppp) cc_final: 0.5800 (ppp) REVERT: C 2593 MET cc_start: 0.7804 (mmp) cc_final: 0.7521 (mmp) REVERT: D 1551 MET cc_start: 0.3098 (mmt) cc_final: 0.1111 (ptt) outliers start: 154 outliers final: 140 residues processed: 604 average time/residue: 1.6273 time to fit residues: 1672.9416 Evaluate side-chains 604 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 464 time to evaluate : 8.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1664 LYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1901 TYR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain A residue 2595 LYS Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 838 GLU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1239 ASN Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 1895 GLN Chi-restraints excluded: chain B residue 1901 TYR Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 700 ASN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1048 ASP Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1882 GLU Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2045 SER Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 LYS Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1320 MET Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1589 LYS Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 1895 GLN Chi-restraints excluded: chain D residue 1901 TYR Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1909 GLN Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2183 GLU Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 792 optimal weight: 10.0000 chunk 834 optimal weight: 9.9990 chunk 761 optimal weight: 8.9990 chunk 811 optimal weight: 9.9990 chunk 488 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 chunk 637 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 733 optimal weight: 3.9990 chunk 767 optimal weight: 5.9990 chunk 809 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN B 562 HIS ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 74312 Z= 0.337 Angle : 0.549 6.218 100488 Z= 0.300 Chirality : 0.036 0.147 11548 Planarity : 0.003 0.087 12756 Dihedral : 4.996 89.101 9992 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.14 % Allowed : 18.84 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.09), residues: 8952 helix: 2.25 (0.07), residues: 5680 sheet: -0.86 (0.20), residues: 612 loop : -0.18 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2196 HIS 0.007 0.001 HIS C1773 PHE 0.020 0.002 PHE A2513 TYR 0.020 0.001 TYR A 17 ARG 0.017 0.001 ARG D1226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 636 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 463 time to evaluate : 8.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1551 MET cc_start: 0.3973 (tpp) cc_final: 0.3313 (mtt) REVERT: B 1551 MET cc_start: 0.6101 (mmm) cc_final: 0.4176 (pmm) REVERT: B 2460 MET cc_start: 0.6928 (tpp) cc_final: 0.6664 (tpp) REVERT: C 1221 MET cc_start: 0.6093 (ppp) cc_final: 0.5749 (ppp) REVERT: C 2314 MET cc_start: 0.6299 (ttp) cc_final: 0.5957 (mtp) REVERT: D 1335 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: D 1551 MET cc_start: 0.3038 (mmt) cc_final: 0.1080 (ptt) outliers start: 173 outliers final: 154 residues processed: 613 average time/residue: 1.5846 time to fit residues: 1661.7478 Evaluate side-chains 607 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 452 time to evaluate : 8.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1664 LYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1895 GLN Chi-restraints excluded: chain A residue 1901 TYR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2183 GLU Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2595 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 838 GLU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1239 ASN Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1587 ASP Chi-restraints excluded: chain B residue 1645 SER Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 1895 GLN Chi-restraints excluded: chain B residue 1901 TYR Chi-restraints excluded: chain B residue 2045 SER Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2159 THR Chi-restraints excluded: chain B residue 2170 ASP Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 700 ASN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1882 GLU Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2045 SER Chi-restraints excluded: chain C residue 2170 ASP Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1222 MET Chi-restraints excluded: chain D residue 1320 MET Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1589 LYS Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1760 LEU Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 1895 GLN Chi-restraints excluded: chain D residue 1901 TYR Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1909 GLN Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2183 GLU Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 533 optimal weight: 7.9990 chunk 858 optimal weight: 6.9990 chunk 524 optimal weight: 5.9990 chunk 407 optimal weight: 2.9990 chunk 596 optimal weight: 10.0000 chunk 900 optimal weight: 1.9990 chunk 828 optimal weight: 9.9990 chunk 717 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 553 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 74312 Z= 0.189 Angle : 0.494 10.435 100488 Z= 0.260 Chirality : 0.034 0.142 11548 Planarity : 0.003 0.050 12756 Dihedral : 4.709 82.005 9992 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.62 % Allowed : 19.30 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.09), residues: 8952 helix: 2.59 (0.07), residues: 5676 sheet: -0.82 (0.20), residues: 628 loop : 0.12 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1127 HIS 0.004 0.001 HIS D1962 PHE 0.021 0.001 PHE A1082 TYR 0.010 0.001 TYR C 872 ARG 0.009 0.000 ARG D1226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue LYS 1040 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Evaluate side-chains 593 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 462 time to evaluate : 8.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1551 MET cc_start: 0.3864 (tpp) cc_final: 0.3277 (mtt) REVERT: B 1348 MET cc_start: 0.6675 (ptp) cc_final: 0.6314 (ptm) REVERT: B 1551 MET cc_start: 0.6046 (mmm) cc_final: 0.4151 (pmm) REVERT: B 2460 MET cc_start: 0.6836 (tpp) cc_final: 0.6577 (tpp) REVERT: D 1551 MET cc_start: 0.2991 (mmt) cc_final: 0.1053 (ptt) outliers start: 131 outliers final: 129 residues processed: 572 average time/residue: 1.5636 time to fit residues: 1520.7127 Evaluate side-chains 587 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 458 time to evaluate : 8.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1382 TYR Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1664 LYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1901 TYR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2041 ASN Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2201 MET Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1239 ASN Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1425 GLU Chi-restraints excluded: chain B residue 1645 SER Chi-restraints excluded: chain B residue 1777 MET Chi-restraints excluded: chain B residue 1895 GLN Chi-restraints excluded: chain B residue 1901 TYR Chi-restraints excluded: chain B residue 2065 LYS Chi-restraints excluded: chain B residue 2159 THR Chi-restraints excluded: chain B residue 2303 ASN Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 489 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 700 ASN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1055 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1239 ASN Chi-restraints excluded: chain C residue 1362 LEU Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1655 MET Chi-restraints excluded: chain C residue 1785 PHE Chi-restraints excluded: chain C residue 1882 GLU Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1924 LEU Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2020 LEU Chi-restraints excluded: chain C residue 2041 ASN Chi-restraints excluded: chain C residue 2182 MET Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1179 LEU Chi-restraints excluded: chain D residue 1320 MET Chi-restraints excluded: chain D residue 1335 PHE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1485 SER Chi-restraints excluded: chain D residue 1595 LEU Chi-restraints excluded: chain D residue 1645 SER Chi-restraints excluded: chain D residue 1777 MET Chi-restraints excluded: chain D residue 1895 GLN Chi-restraints excluded: chain D residue 1901 TYR Chi-restraints excluded: chain D residue 1909 GLN Chi-restraints excluded: chain D residue 2004 MET Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2225 TYR Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 569 optimal weight: 7.9990 chunk 763 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 661 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 718 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 737 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2289 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1696 GLN ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 GLN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.065374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.049087 restraints weight = 1274975.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.049629 restraints weight = 511201.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.049790 restraints weight = 394970.136| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 74312 Z= 0.469 Angle : 0.620 8.131 100488 Z= 0.344 Chirality : 0.038 0.198 11548 Planarity : 0.004 0.071 12756 Dihedral : 4.985 83.614 9992 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.89 % Allowed : 19.19 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 8952 helix: 1.92 (0.07), residues: 5704 sheet: -1.09 (0.20), residues: 628 loop : -0.42 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 219 HIS 0.008 0.001 HIS C1884 PHE 0.025 0.002 PHE B 244 TYR 0.028 0.002 TYR A 17 ARG 0.010 0.001 ARG D1226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30214.86 seconds wall clock time: 523 minutes 7.75 seconds (31387.75 seconds total)